RNAalifold Output Files

	4 sequence; length of alignment 78
	alifold output
	    6    72  0  99.8%   0.006 GC:2    GU:1    AU:1   
	   33    43  0  99.0%   0.030 GC:2    GU:1    AU:1   
	   31    45  0  99.2%   0.027 CG:3    UA:1   
	    5    73  1  99.7%   0.008 CG:2    GC:1   
	   15    25  0  98.6%   0.055 CG:3    UA:1   
	    7    71  0  98.5%   0.044 GC:1    AU:2    --:1   
	   30    46  0  98.5%   0.045 CG:2    UA:2   
	    4    74  1  99.6%   0.011 CG:3   
	[...]

The last output file produced by RNAalifold -p, named alifold.out, is a plain text file with detailed information on all plausible base pairs sorted by the likelihood of the pair. In the example above we see that the pair $(6,72)$ has no inconsistent sequences, is predicted almost with probability 1, and occurs as a GC pair in two sequences, a GU pair in one, and a AU pair in another.

RNAalifold automatically produces a drawing of the consensus structure in Postscript format and writes it to the file ``alirna.ps''. In the structure graph consistent and compensatory mutations are marked by a circle around the variable base(s), i.e. pairs where one pairing partner is encircled exhibit consistent mutations, whereas pairs supported by compensatory mutations have both bases marked. Pairs that cannot be formed by some of the sequences are shown gray instead of black. In the example given, many pairs show such inconsistencies. This is because one of the sequences (AF346993) is not aligned well by clustalw.

Note, that subsequent calls to RNAalifold will overwrite any existing output alirna.ps (alidot.ps, alifold.out) files in the current directory. Be sure to rename any files you want to keep.